Pogorelov, T. V. | bioRxiv Science

bioRxiv2022

Cytoplasmic folding, mis-folding, and early stages of aggregation

We examine how cellular interactions in an all-atom model of the Homo sapiens cytoplasm influence the early folding events of Protein B (PB), a three-helix bundle protein. While PB is known to fold during in vitro simulations in three microseconds, all three initially unfolded PB copies in our cytoplasm model never completely reached their native topology across our 31 microsecond simulation. We were able to capture initial formation of all three helices and a compact topology similar to the native state. Sticking interactions between PB and surrounding macromolecules, as well as other unfolded PBs, became competitive with PB folding. Interaction between PB copies seeded beta-strand formation, modeling initial events of protein aggregation. Finally, the fold-switching potential of PB related GA domains has been explored in previous studies, and the sticking and crowding in our model thus initiates sampling of helix/sheet structural plasticity of PB.

biophysics↗

bioRxiv2020

Proteins and Ions Compete for Membrane Interaction: the case of Lactadherin

Charged molecular species, such as ions, play a vital role in the life of the cell. In particular, divalent calcium ions (Ca2+) are critical for activating cellular membranes. Interactions between Ca2+ and anionic phosphatidylserine (PS) lipids result in structural changes of the plasma membrane and are vital for many signaling pathways, such as the tightly regulated blood coagulation cascade. Upon cell damage, PS lipids are externalized to the outer leaflet, where they are not only exposed to Ca2+, but also to proteins. Lactadherin is a glycoprotein, important for cell-adhesion, that can act as an anticoagulant. While a number of experimental studies have been performed on lactadherins C2 domains (LactC2) binding affinity for PS molecules, an atomistic description of LactC2 interactions with PS lipids in the plasma membrane is lacking. We performed extensive all-atom molecular dynamics simulations of mixed lipid bilayers and experimental characterization of LactC2-membrane interactions in the presence and absence of Ca2+ and characterized PS-Ca2+ and PS-LactC2 interactions to guide our understanding of how these interactions initiate and impede blood coagulation, respectively. The captured spontaneously formed long-lived PS-Ca2+ and PS-LactC2 complexes revealed that the protein side chains involved in PS-LactC2 interactions appear to be affected by the presence of Ca2+. The degree of LactC2 insertion into the lipid bilayer also appears to be dependent on the presence of Ca2+. Characterizing the interactions between Ca2+ and LactC2 with PS lipids can lead to a greater understanding of the activation and regulation of the blood coagulation cascade and of the basis of charged species interactions with the lipid membrane. STATEMENT OF SIGNIFICANCELactadherin plays an important role in cellular signaling including blood coagulation. Many of these processes involve lactadherin interacting with the lipids of the cell plasma membrane. Lactadherin acts as an anticoagulant and contributes to a number of health issues. Understanding the interactions that drive lactadherins anticoagulant properties can lead to potential new drug targets.

biophysics↗